rs16894458

Variant names:

• chr5-61740609-T-A
• rs16894458
• ENST00000507461.2:n.140-7993T>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000507461.2(C5orf64):​n.140-7993T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0637 in 152,298 control chromosomes in the GnomAD database, including 573 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (573 hom., cov: 32)
• Consequence: C5orf64 ENST00000507461.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450

Genes affected

C5orf64 (HGNC:26744): (long intergenic non-protein coding RNA 3122) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C5orf64	ENST00000507461.2	n.140-7993T>A		intron_variant	Intron 1 of 4	4
C5orf64	ENST00000655479.2	n.149-7993T>A		intron_variant	Intron 2 of 4
C5orf64	ENST00000656556.1	n.113-7993T>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.0635 AC: 9668 AN: 152180 Hom.: 566 Cov.: 32

Gnomad AFR AF: 0.133

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0768

Gnomad ASJ AF: 0.0360

Gnomad EAS AF: 0.0893

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.0138

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0203

Gnomad OTH AF: 0.0522

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0637 AC: 9699 AN: 152298 Hom.: 573 Cov.: 32 AF XY: 0.0648 AC XY: 4828 AN XY: 74474

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.0772

Gnomad4 ASJ AF: 0.0360

Gnomad4 EAS AF: 0.0889

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0138

Gnomad4 NFE AF: 0.0203

Gnomad4 OTH AF: 0.0521

Alfa AF: 0.0447 Hom.: 38

Bravo AF: 0.0701

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.2
DANN	Benign	0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs16894458; hg19: chr5-61036436; COSMIC: COSV72696654;